From ece56c026ee46b81fae8c8d9948775ed8b7a947e Mon Sep 17 00:00:00 2001
From: KristinaGomoryova <gomoryova@sci.muni.cz>
Date: Wed, 3 Jul 2024 10:45:12 +0200
Subject: [PATCH] ruff errors resolved

---
 pyproject.toml                      | 16 +++++------
 src/rcx_tk/process_metadata_file.py | 44 +++++++++++++++--------------
 2 files changed, 31 insertions(+), 29 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9bfad9b..f645889 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ extras = dev
 
 [tool.ruff]
 # Enable Pyflakes `E` and `F` codes by default.
-select = [
+lint.select = [
     "F",  # Pyflakes
     "E",  # pycodestyle (error)
     "W",    # pycodestyle (warning)
@@ -57,7 +57,7 @@ select = [
     # "PLW",  # Warning
 
 ]
-ignore = [
+lint.ignore = [
     'D100',  # Missing module docstring
     'D104',  # Missing public package docstring
     # The following list excludes rules irrelevant to the Google style
@@ -76,8 +76,8 @@ ignore = [
 ]
 
 # Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ["A", "B", "C", "D", "E", "F", "I"]
-unfixable = []
+lint.fixable = ["A", "B", "C", "D", "E", "F", "I"]
+lint.unfixable = []
 
 exclude = [
     ".bzr",
@@ -102,16 +102,16 @@ exclude = [
     ".venv",
     "scripts",
 ]
-per-file-ignores = {}
+lint.per-file-ignores = {}
 
 
 # Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
 target-version = "py39"
 line-length = 120
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ["rcx_tk"]
 force-single-line = true
 no-lines-before = ["future","standard-library","third-party","first-party","local-folder"]
@@ -129,4 +129,4 @@ filename = "pyproject.toml"
 filename = "CITATION.cff"
 
 [[tool.bumpversion.files]]
-filename = "docs/conf.py"
\ No newline at end of file
+filename = "docs/conf.py"        
\ No newline at end of file
diff --git a/src/rcx_tk/process_metadata_file.py b/src/rcx_tk/process_metadata_file.py
index b0d9ced..eb9314d 100644
--- a/src/rcx_tk/process_metadata_file.py
+++ b/src/rcx_tk/process_metadata_file.py
@@ -1,54 +1,56 @@
-import pandas as pd
 import os
+import pandas as pd
+
 
 def read_file(file_path):
     """Reads a file and returns a DataFrame based on the file extension."""
     file_extension = os.path.splitext(file_path)[1].lower()
-    if file_extension == '.csv':
+    if file_extension == ".csv":
         return pd.read_csv(file_path)
-    elif file_extension in ['.xls', '.xlsx']:
+    elif file_extension in [".xls", ".xlsx"]:
         return pd.read_excel(file_path)
-    elif file_extension == '.txt':
-        return pd.read_csv(file_path, sep='\t')
+    elif file_extension == ".txt":
+        return pd.read_csv(file_path, sep="\t")
     else:
         raise ValueError("Unsupported file format. Please provide a CSV, Excel, or TSV file.")
 
+
 def save_dataframe_as_tsv(df, file_path):
     """Saves a DataFrame as a TSV file."""
-    output_file = f'processed_{os.path.splitext(os.path.basename(file_path))[0]}.tsv'
-    df.to_csv(output_file, sep='\t', index=False)
+    output_file = f"processed_{os.path.splitext(os.path.basename(file_path))[0]}.tsv"
+    df.to_csv(output_file, sep="\t", index=False)
     print(f"Processed file saved as: {output_file}")
 
+
 def process_metadata_file(file_path):
     """Processes a metadata file, keeping and renaming specific columns."""
     columns_to_keep = {
-        'File name': 'sampleName',
-        'Type': 'sampleType',
-        'Class ID': 'class',
-        'Batch': 'batch',
-        'Analytical order': 'injectionOrder'
+        "File name": "sampleName",
+        "Type": "sampleType",
+        "Class ID": "class",
+        "Batch": "batch",
+        "Analytical order": "injectionOrder",
     }
-    
+
     df = read_file(file_path)
     df = df[list(columns_to_keep.keys())].rename(columns=columns_to_keep)
-    df['sampleName'] = df['sampleName'].str.replace(' ', '_')
+    df["sampleName"] = df["sampleName"].str.replace(" ", "_")
     save_dataframe_as_tsv(df, file_path)
 
+
 def process_alkane_ri_file(file_path):
     """Processes an Alkane RI file, keeping and renaming specific columns."""
-    columns_to_keep = {
-        'Carbon number': 'carbon_number',
-        'RT (min)': 'rt'
-    }
-    
+    columns_to_keep = {"Carbon number": "carbon_number", "RT (min)": "rt"}
+
     df = read_file(file_path)
     df.columns = df.columns.str.strip()
     df = df.rename(columns=columns_to_keep)
     save_dataframe_as_tsv(df, file_path)
 
+
 # File paths
-metadata_file_path = 'metadata file path'
-alkane_file_path = 'alkane file path'
+metadata_file_path = "metadata file path"
+alkane_file_path = "alkane file path"
 
 # Process files
 process_metadata_file(metadata_file_path)